Prentice Hall c2002Chapter 11 Principles of Biochemistry Fourth Edition Chapter 1: Introduction to...

Prentice Hall c2002 Chapter 1 1

Principles of BiochemistryFourth Edition

Chapter 1:Introduction to Biochemistry

Copyright © 2006 Pearson Prentice Hall, Inc.

Horton • Moran • Scrimgeour • Perry • Rawn

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Chapter 1 Introduction to Biochemistry

• Adenovirus: Viruses consist of a nucleic acid molecule surrounded by a protein coat

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1.1 Biochemistry Is a Modern Science

• Urea (尿素 ) was synthesized by heating the inorganic compound ammonium cyanate (1828)

• This showed that compounds found exclusively in living organisms could be synthesized from common inorganic substances

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In 1897 Eduard Buchner showed that extracts of yeast cells could catalyze the fermentation of the sugar glucose to alcohol and carbon dioxide.

Fischer described enzymes as rigid templates, or locks, and substrates as matching keys.

The last half of the 20th century saw tremendous advances in the area of structural biology, especially the structure of proteins.

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Two notable breakthroughs in the history of biochemistry

(1) Discovery of the role of enzymes as catalysts

(2) Identification of nucleic acids as information molecules

Flow of information: from nucleic acids to proteins

DNA RNA Protein

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In 1944 Oswald Avery et al. provided the first conclusive evidence that DNA is the genetic material.

In 1953 Watson and Crick deduced the three-dimensional structure of DNA

In 1958, Crick proposed the Central Dogmal of molecular biology.

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1.2 The Chemical Elements of Life

• Only six nonmetallic elements: oxygen, carbon, hydrogen, nitrogen, phosphorous, and sulfur account for >97% of the weight of most organisms

• These elements can form stable covalent bonds

• Water is a major component of cells

• Carbon is more abundant in living organisms than it is in the rest of the universe

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Fig 1.1 Periodic Table of the elements

• Important elements found in living cells are shown in color

• The six abundant elements are in red (CHNOPS)

• Five essential ions are in purple

• Trace elements are in dark blue (more common) and light blue (less common)

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Functional groups in biochemistry

• Functional groups (官能基 )- specific parts of molecules involved in biochemical reactions

• Figure 1.2 shows the general formulas of:

(a) Organic compounds

(b) Functional groups

(c) Linkages common in biochemistry

(R represents an alkyl group (CH3CH2)n-)

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Fig 1.2 (a) General formulas

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Fig 1.2(b) General Formulas

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Fig 1.2 (c) General Formulas

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1.3 Many Important Biomolecules are Polymers

• Biopolymers - macromolecules created by joining many smaller organic molecules (monomers)

• Condensation reactions (縮合反應 ) join monomers (H2O is removed in the process)

• Residue (殘基 )- each monomer in a chain

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Molecular mass

• Molecular weight is more correctly termed the relative molecular mass (Mr) - the molecular mass relative to 1/12 mass of a carbon atom (12C)

• Mr is a relative quantity and is dimensionless

• A typical protein may have an Mr = 38,000

• The absolute molecular mass of this protein = 38,000 daltons (1 dalton = 1 atomic mass unit)

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A. Proteins

• Proteins are composed of 20 common amino acids

• Each amino acid contains:

(1) Carboxylate group (-COO-)

(2) Amino group (-NH2)

(3) Side chain (R) unique to each amino acid

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Fig 1.3 Structure of an amino acid and a dipeptide

(a) Amino group (blue), carboxylate group (red)

(b) Dipeptides are connected by peptide bonds

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Polypeptides

• Polypeptides - amino acids joined end to end

• Conformation (構形 )- the three dimensional shape of a protein which is determined by its sequence

• Active site - a cleft or groove in an enzyme that binds the substrates of a reaction

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Fig 1.4 Egg white lysozyme

(a) Free enzyme

(b) Enzyme, bound substrate in active site cleft

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B. Polysaccharides

• Carbohydrates, or saccharides, are composed primarily of C,H and O

• Polysaccharides are composed of saccharide monomers

• Most sugar structures can be represented as either linear (Fischer projection) or cyclic

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Fig 1.5 Representations of the structure of ribose

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Fig 1.6 (a) Glucose, (b) Cellulose

Glycosidic bonds connecting glucose residues are in red

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C. Nucleic Acids

• Polynucleotides - nucleic acid biopolymers are composed of nucleotide monomers

• Nucleotide monomers are composed of:

(1) A five-carbon sugar

(2) A heterocyclic nitrogenous base

(3) Phosphate group(s)

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Fig 1.7 Deoxyribose

• Deoxyribose lacks a hydroxyl group at C-2. It is the sugar found in DNA.

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Nitrogenous bases

• Major Purines:

Adenine (A)

Guanine (G)

• Major Pyrimidines

Cytosine (C)

Thymine (T)

Uracil (U)

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Fig 1.8 Adenosine Triphosphate (ATP)

• Nitrogenous base (adenine), sugar (ribose)

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Fig 1.9 Structure of a dinucleotide

• Residues are joined by a phosphodiester linkage

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Fig 1.10 Short segment of a DNA molecule

• Two polynucleotides associate to form a double helix (雙螺旋 )

• Genetic information is carried by the sequence of base pairs

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D. Lipids and Membranes

• Lipids are rich in carbon and hydrogen, but contain little oxygen

• Lipids are not soluble in water

• Fatty acids are the simplest lipids: long chain hydrocarbons, a carboxylate group at one end

• Fatty acids are often components of glycerophospholipids

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Fig 1.11 Structures of (a) glycerol 3-phosphate, (b) a glycerophospholipid

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Fig 1.12 Model of a membrane lipid

• Hydrophilic (water-loving 親水性 ) head interacts with H2O

• Hydrophobic (water-fearing 忌水性 ) tail

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Fig 1.13 Structure of a biological membrane

• A lipid bilayer with associated proteins

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1.4 The Energetics of Life

• Photosynthetic organisms capture sunlight energy and use it to synthesize organic compounds

• Organic compounds provide energy for all organisms

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Energy Flow

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Metabolism and energy

• Metabolism - collection of reactions by which organic compounds are synthesized and degraded

• Bioenergetics - study of the changes in energy during metabolic reactions

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Free energy (G)

• Free energy change (G) can predict the equilibrium concentrations and direction of a reaction where:H = enthalpy change, S = entropy change, T = temp

• When G<0, the reaction will proceed spontaneously in the direction written

• When G>0, the reaction requires energy to proceed

G = H - TS

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1.5 Biochemistry and Evolution

• Prokaryotes (原核生物 )- do not have a membrane-bounded nucleus

• Eukaryotes ( 真核生物 ) - possess nucleus and other complex internal structures

• Prokaryotes and eukaryotes appear to have evolved from a common ancestor over three billion years ago

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1.6 The Cell is the Basic Unit of Life

• Plasma membrane - surrounds aqueous environment of the cell

• Cytoplasm - all materials enclosed by the plasma membrane (except the nucleus)

• Cytosol - aqueous portion of the cytoplasm minus subcellular structures

• Bacteriophage or phage - viruses that infect prokaryotic cells

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1.7 Prokaryotic Cells: Structural Features

• Prokaryotes, or bacteria are usually single-celled organisms

• Prokaryotes lack a nucleus (their DNA is packed in a nucleoid region of the cytoplasm)

• Escherichia coli (E. coli) - one of the best studied of all living organisms

• E. coli cells are ~0.5m diameter, 1.5m long

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Fig. 1.14 E. coli cell

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1.8 Eukaryotic Cells: Structural Features

• Eukaryotes: plants, animals, fungi, protists

• Have a membrane-enclosed nucleus containing the chromosomes

• Are commonly 1000-fold greater in volume than prokaryotic cells

• Have an intracellular membrane network that subdivides the interior of the cell

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Fig 1.15 (a) Eukaryotic cell (animal)

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Fig 1.15(b) Eukaryotic cell (plant)

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A. The Nucleus

Nuclear envelope and endoplasmic reticulum of a eukaryotic cell

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B. Endoplasmic Reticulum and Golgi Apparatus

• Endoplasmic reticulum (內質網 )- network of membrane sheets and tubules extending from the nucleus

• Golgi apparatus (高氏體 )- responsible for modification and sorting of some biomolecules.

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Golgi apparatus

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C. Mitochondria and Chloroplasts

• Mitochondria (粒線體 ) are the main sites of energy transduction in aerobic cells.

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Chloroplasts (葉綠體 )- sites of photosynthesis in plants, green algae

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D. Specialized Vesicles

• Lysosomes (溶素體 )- contain specialized digestive enzymes

• Peroxisomes - carry out oxidative reactions in animal and plant cells

• Vacuoles (液泡 )- fluid-filled vesicles, used as storage sites for water, ions and nutrients such as glucose

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E. The Cytoskeleton

• A protein scaffold is required for support, internal organization and movement of a cell

• Actin filaments form ropelike threads

• Microtubules are rigid fibers packed into bundles

- Serve as an internal skeleton

- Form the mitotic spindle during mitosis

- Form movement structures (e.g. cilia, flagella)

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Fig 1.16

Fluorescently labeled:(a) Actin filaments

(b) Microtubules

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1.9 A Picture of Living Cell

Fig 1.17 Cytosol of an E. coli cell.

Magnification:

Top 106X

Bottom 107X (shows water, other small molecules)

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1.10 Biochemistry is Multidisciplinary

• Various disciplines contribute to understanding biochemistry:

Physics Genetics

Chemistry Physiology

Cell biology Evolution

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Textbook organization

• Horton is organized into four sections:

1. PART ONE: Introduction

2. PART TWO: Structure and Function of Biomolecules

3. PART THREE: Metabolism and Bioenergetics

4. PART FOUR: Biological Information Flow

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